Harvesting microbes from the ruins of a ghost town

Harvesting microbes from the ruins of a ghost town
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    - [Narrator] Centralia Pennsylvania is a ghost town.
    Nearly 3000 people used to live here,
    but these days it's almost completely abandoned.
    And it's pretty eerie but that's okay
    because what we're looking for
    is actually in the soil.
    Some 100 meters below us
    an underground fire is burning away.
    It's what turned Centralia into a ghost town.
    But while almost all of the people have fled,
    some tiny microbes have appeared.
    Among them, thermophiles, critters that live
    at super hot temperatures.
    We're hoping to collect some thermophiles
    and grow them in our studio.
    We'll look at what happens to life in extreme environments.
    - I think we should take a sample here.
    - [Narrator] And we'll get a glimpse
    into what microbes might be hiding in soil
    all over the world, waiting patiently
    for a calamity to call their own.
    - Oh yeah you can actually feel that
    there's a little bit of steam.
    I don't think the cameras can pick it up.
    - [Narrator] Our mission today is to collect
    a couple types of microbes from the soil.
    Bacteria and archaea.
    We're working in the footsteps of a researcher
    from Michigan State University named Ashley Shade.
    She's the principal investigator on a recent paper
    that looks at microbes here in Centralia.
    It's an effort to understand what happens
    to microbial communities when, for example,
    the ground itself catches fire and burns for decades.
    - And so the big premise, the big question
    was about how did those systems respond
    and are they capable of recovering
    from such a sledgehammer of a disturbance?
    - [Narrator] The story of what happened here
    is dramatic.
    Centralia was a mining town,
    but the coal mine that supported it
    was largely exhausted by the 1960s.
    The fire actually had nothing to do with mining.
    In the summer of 1962, some burning garbage
    at a nearby landfill ignited the coal seam
    that remained under the area.
    This set off a massive subterranean blaze
    that proved extremely difficult to contain.
    The fire encroached on the town year over year,
    venting dangerous gas into the air,
    and ripping fissures in the local highway.
    - I think now you can tell why they closed the highway down.
    - [Narrator] People began to flee in earnest in the 1980s,
    and today, the government has relocated
    almost all its residents.
    What happened in Centralia was disastrous,
    but it also set in motion the science
    we're here for today.
    - The vegetation has changed.
    It doesn't look like it's that much different
    but you can feel the ground,
    it's much softer than it was on the other side of the road.
    - [Narrator] Once we were all set up,
    we sterilized our tools and got to work.
    Finding active fire areas is tricky
    because again, the fires are underground,
    so we basically looked for hot soil.
    - Unfortunately there's no steam
    'cause it's not cold enough outside,
    but this would be a good candidate for a place
    I think to take a soil sample.
    - [Narrator] We hiked around a little.
    - I want to go take some readings in here.
    - [Narrator] We hitched a ride to a sinkhole
    from a guy in an off-road vehicle,
    and we generally combed over the area from Ashley's study.
    - So we're at the St. Ignatius cemetery now.
    A lot of the papers that we read
    talked about the turquoise zone
    which is the ridge just north of the cemetery,
    and that's where they found a lot of the hottest readings,
    so we're gonna go take a couple samples in that zone
    and see what we can find.
    - [Narrator] But site after site,
    and reading after reading, we didn't find much.
    - It's kind of cool right now,
    but I think we should take a sample.
    - This ain't it.
    - Alright, I'm getting colder over here.
    Maybe the fire is finally gone after all these years.
    (laughs) I don't think that's the case.
    - [Narrator] We were hoping for soil
    that was maybe 40 or 50 degrees Celsius,
    but we kept finding 15 to 20.
    It was barely warmer than the air,
    so we called Ashley's research assistant Keara
    for help in real time.
    - [Keara] What I was kind of hoping would maybe
    would be get into video chat and have you look around
    or something.
    What might work is if you just kind of be the eyes
    and I can walk you to some places.
    It's all just stuff that lives in my brain.
    - You're on camera.
    - [Keara] Oh hello, hi!
    - It's an adventure.
    - [Narrator] Keara led us to a couple new spots.
    - [Keara] Somewhere up ahead and to the right.
    - [Narrator] We dug a little deeper,
    and finally found some promising soil.
    - Now I'm getting a reading of about 27 degrees Celsius.
    That goes pretty deep in there too.
    - [Narrator] Now 27 degrees Celsius might be low
    for finding thermophiles,
    there are plenty who thrive in places twice as hot,
    but it was abnormally warm for Pennsylvania soil in March,
    so we grabbed some samples, put them on ice
    to keep the microbes at rest,
    and headed home to grow them.
    So the first step to regrowing our microbes
    is getting them out of the soil,
    and that part's pretty easy.
    We just mash up the clumps, add some distilled water
    to create slurry, and shake everything up.
    Once the slurry settles, there should be
    plenty of microbes floating around in the water.
    This part's trickier.
    We dilute the sample by different amounts,
    and grow a Petri dish full of microbes using each dilution.
    The idea is to grow enough microbes to study
    but not so many that they'll take over the Petri dish.
    With our samples prepped,
    we spread a bit of liquid from each dilution
    onto a Petri dish filled with nutrient-rich gel.
    We're growing microbes from a couple hot soil areas
    and also from a place that was
    never exposed to Centralia's heat.
    That's our control group.
    Ashley and Keara did grow some microbes of their own
    just like we're doing, but it gives them
    a pretty incomplete picture of what's there.
    - So that's because we can't culture
    99% of the bacteria and archaea that are found in soil
    just because we don't know how to,
    we're unable to bring them into the lab.
    - [Narrator] It's a mystery that
    lots of scientists puzzle over.
    Many microbes just refuse to grow in a lab environment.
    So Ashley's team resorts to higher tech methods.
    - What we do is we extract all of the DNA from the soil,
    and then we sequence it.
    And we use that sequencing information
    to put together whole genomes of organisms
    that lived in that soil.
    - [Narrator] By sorting through all the DNA present,
    they can look for trends in the samples.
    Ashley's team collected samples
    from a range of temperature areas in Centralia.
    Places that were hot, others that cooled back down,
    and others still that were
    never affected by the fire.
    That way they could sniff out correlations between things
    like temperature and genome size.
    Our final step is to pop all of these samples
    into our incubator.
    We're going to grow them at around 55 degrees Celsius
    for two to three days.
    Some samples might take longer.
    After three days, we checked our little microbe oven.
    - Oh, so gross, oh.
    - [Narrator] And we got to work filming the samples
    so we could ask Ashley and Keara what we found.
    Again, this isn't quite how Ashley did it.
    Once her team sorted through their DNA,
    they checked it against available DNA libraries,
    and a surprising amount of the DNA they found
    is a mystery.
    - I'd say about 30% of what we find is unclassified.
    We know that they're bacteria or archaea,
    but we don't know anything else other than that.
    - [Narrator] For the record, bacteria and archaea
    are domains of life, which is basically
    the broadest category.
    - And so that's like basically saying
    I've identified this organism,
    but I don't know enough about it
    to tell whether or not it's a jellyfish,
    a human or a tree.
    - That said, they are learning a ton from their collections.
    One big takeaway is the thermophiles they found
    tended towards smaller genome sizes
    and smaller cell sizes.
    It's not totally clear why,
    but one popular theory is that it's just
    easier to maintain smaller hardware at higher temperatures.
    - And so the idea is that if you can keep your cells small,
    you are going to benefit by not having to
    spend so much energy just maintaining
    all of your cell parts which are kind of
    getting more wobbly at the higher temperatures.
    - So what exactly did we find?
    Well first our hot samples grew a lot more
    than our cold control group did,
    and there's a logic to that.
    We regrew all the samples at a pretty high temperature
    and the microbes that seemed happiest with that
    came from the hot soil.
    But overall, eyeballing microbial life is tough.
    Keara was pretty confident that these structures here
    are bacteria, but it's hard to say much more than that.
    This is exactly why DNA sequencing
    is where most of the science happens.
    There may well be thermophiles
    growing in these Petri dishes,
    but we'll need a lot more tech to point them out.
    After this whole process, our biggest question
    was okay Centralia caught fire
    and a bunch of microbes appeared to capitalize on that,
    but where on earth did they come from?
    There wasn't nearly enough time for the microbes here
    to evolve a heat tolerance, so what's going on?
    - This is a question that a lot of people
    are curious about because you can find thermophiles
    in the coldest weirdest places on the planet Earth.
    You can find them in the permafrost, right?
    You can find them in the deep ocean cold sediments,
    you can pull out some thermophile spores
    and resuscitate them at hot temperatures.
    - Ashley's guess is that these microbes
    have been in Pennsylvania dormant for a long time.
    Where they originally came from and when
    is a total mystery, but it suggests that wherever you look
    there might be dormant life
    that thrives in extreme temperatures.
    And as the planet warms,
    these questions become more pertinent.
    Even a couple degrees could change the dynamic
    within microbial communities all over the world.
    That might not be disastrous,
    but it's worth understanding.
    If every community has its optimum temperature,
    we could see spikes all over in microbes
    that are doing the same thing
    that thermophiles in Centralia did,
    lying dormant, and waiting.
    - That's a good way of talking about it.
    They are definitely playing the long game.
    - We should make an executive decision
    if I'm using Fahrenheit or Celsius.
    I'm all over the place.
    I'll keep this on Celsius.
    I just when I see 24, it's gonna be a (bleep)ing
    disaster to edit. (laughs)
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